chr17-35987850-G-T

Variant names:

• chr17-35987850-G-T
• rs10491118
• ENST00000612584.1:n.1458G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000612584.1(ENSG00000275431):​n.1458G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0959 in 152,192 control chromosomes in the GnomAD database, including 770 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.096 (770 hom., cov: 32)
  • Exomes 𝑓: 0.071 (0 hom.)
• Consequence: ENSG00000275431 ENST00000612584.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.143
• Publications: 12 publications found

Genes affected

ENSG00000275431 (HGNC:):

CCL15-CCL14 (HGNC:44436): (CCL15-CCL14 readthrough (NMD candidate)) A cluster of CC chemokine genes exists on chromosome 17q11.2. The CC chemokines are secreted proteins characterized by two adjacent cysteines. The genes chemokine (C-C motif) ligand 14 and chemokine (C-C motif) ligand 15 are adjacent loci and express read-through transcripts spanning both loci. The read-through transcripts were originally interpreted as bicistronic transcripts, but they are represented as non-coding because they are candidates for nonsense-mediated mRNA decay (NMD). [provided by RefSeq, Dec 2009]

ENSG00000270240 (HGNC:58767):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000612584.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCL15-CCL14	NR_027921.3		n.935-1146C>A		intron	N/A
	CCL15-CCL14	NR_027922.3		n.935-1146C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000275431	ENST00000612584.1	TSL:1	n.1458G>T		non_coding_transcript_exon	Exon 2 of 2
	CCL15-CCL14	ENST00000616694.1	TSL:2	n.*47-1146C>A		intron	N/A	ENSP00000481402.1
	CCL15-CCL14	ENST00000610751.4	TSL:2	n.*47-1146C>A		intron	N/A	ENSP00000481940.1

Frequencies

GnomAD3 genomes AF: 0.0958 AC: 14571 AN: 152060 Hom.: 769 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.0677

Gnomad ASJ AF: 0.0766

Gnomad EAS AF: 0.0931

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0874

Gnomad OTH AF: 0.0837

GnomAD4 exome AF: 0.0714 AC: 1 AN: 14 Hom.: 0 Cov.: 0 AF XY: 0.100 AC XY: 1 AN XY: 10

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.100 AC: 1 AN: 10

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.0959 AC: 14596 AN: 152178 Hom.: 770 Cov.: 32 AF XY: 0.0996 AC XY: 7406 AN XY: 74388

African (AFR) AF: 0.107 AC: 4422 AN: 41510

American (AMR) AF: 0.0676 AC: 1034 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0766 AC: 266 AN: 3472

East Asian (EAS) AF: 0.0924 AC: 479 AN: 5184

South Asian (SAS) AF: 0.117 AC: 566 AN: 4824

European-Finnish (FIN) AF: 0.150 AC: 1587 AN: 10566

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0874 AC: 5945 AN: 68008

Other (OTH) AF: 0.0848 AC: 179 AN: 2112

Alfa AF: 0.0855 Hom.: 1673

Bravo AF: 0.0893

Asia WGS AF: 0.152 AC: 527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.80
DANN	Benign	0.30
PhyloP100		-0.14
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10491118; hg19: chr17-34314886;